In the last decade, Makerere University (MU) in Kampala, Uganda, has become one of the principal academic institutions worldwide for collaborative research on TB. Currently NIH, CDC, Gates Foundation, Wellcome Trust, British Medical Research Council and the European & Developing Countries Clinical Trials Partnership provide substantial support to TB research in Uganda, including evaluation of new diagnostics; drug treatment regimens; vaccines and translational studies of pathogenesis and correlates of immunity. NIH has supported training in epidemiology; immunology and microbiology related to HIV, while Wellcome Trust funds a capacity-building program in the immunology of tropical diseases. Despite these efforts, training in basic and translational research on TB lags far behind the pressing need. For example, the development of improved TB diagnostics, vaccines and therapies requires the discovery of biomarkers. Uganda is a leading site for research on biomarkers but relies on expatriate scientists for developmental research and often on shipment of specimens for off-site analysis. With development of advanced laboratory infrastructure at MU and other sites in Uganda, the lack of well-trained independent Ugandan scientists conducting basic and translational research at MU is neither necessary nor appropriate. This training program is the product of a needs assessment by academic leaders of MU and Boston University (BU). It is time to provide basic research training to qualified Ugandan scientists equivalent to that available to American graduate students and post-doctoral fellows. As there is growing infrastructure to support independent Ugandan-led research, we have organized this program so that following training, trainees will return to MU as academic faculty and will have the opportunity to establish valuable research programs on tuberculosis and other emerging infectious diseases in Uganda. The Aims of this Program are tailored to address the current and future needs of MU. The capacity-building program helps fill the gaps identified in the needs assessment and addresses priority developmental goals of MU School of Medicine.